[RTR] Muscles changing color with activation #68

EveCharbie · 2025-07-04T13:18:51Z

This change is

blacked

codeclimate · 2025-07-04T13:19:13Z

pyorerun/pyoemg.py

+    A class to handle emg data.
+    """
+
+    def __init__(


Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.

codeclimate · 2025-07-04T13:19:13Z

pyorerun/pyoemg.py

+    A class to handle emg data.
+    """
+
+    def __init__(


Function __init__ has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Ipuch

Reviewed 11 of 11 files at r1, all commit messages.
Reviewable status: all files reviewed, 13 unresolved discussions (waiting on @EveCharbie)

pyorerun/phase_rerun.py line 63 at r1 (raw file):

        q: np.ndarray,
        tracked_markers: PyoMarkers | np.ndarray = None,
        emg: Pyoemg | np.ndarray = None,

PyoMuscles

pyorerun/model_phase.py line 19 at r1 (raw file):

        self.rerun_models = []
        self.q = []
        self.muscle_colors = []

muscle_activations_intensity (?)

pyorerun/model_phase.py line 32 at r1 (raw file):

    def add_animated_model(
        self, model: AbstractModel, q: np.ndarray, tracked_markers: np.ndarray = None, muscle_colors: np.ndarray = None

consistency on names

pyorerun/model_phase.py line 36 at r1 (raw file):

        self.models.append(model)
        self.rerun_models.append(
            ModelUpdater(name=f"{self.name}/{self.nb_models}_{model.name}", model=model, muscle_colors=muscle_colors)

consistency on names

pyorerun/abstract/linestrip.py line 103 at r1 (raw file):

            A numpy array with the color of each line.
        """
        # @ ipuch: at this point we do not know how much frames there will be :/

remove the comment.

pyorerun/__init__.py line 19 at r1 (raw file):

from .phase_rerun import PhaseRerun
from .pyomarkers import Pyomarkers
from .pyoemg import Pyoemg

PyoMuscles

pyorerun/model_components/ligaments.py line 72 at r1 (raw file):

            colors = [self.properties.color[s, :, :] for _ in range(nb_frames) for s in range(self.nb_strips)]
        else:
            colors = [self.properties.color for _ in range(nb_frames * self.nb_strips)]

def color_to_rerun(nb_frame):
return

Code quote:

        # @ipuch: I do not find the declaration, but I feel this should be done before
        if len(self.properties.color.shape) == 3:
            colors = [self.properties.color[s, f, :] for f in range(nb_frames) for s in range(self.nb_strips)]
        elif len(self.properties.color.shape) == 2:
            colors = [self.properties.color[s, :, :] for _ in range(nb_frames) for s in range(self.nb_strips)]
        else:
            colors = [self.properties.color for _ in range(nb_frames * self.nb_strips)]

examples/biorbd/gait_reconstruction.py line 4 at r1 (raw file):

import numpy as np

from pyorerun.pyomarkers import Pyomarkers as PyoMarkers

PyoMarkers

examples/biorbd/gait_reconstruction.py line 6 at r1 (raw file):

from pyorerun.pyomarkers import Pyomarkers as PyoMarkers

from pyorerun import BiorbdModel, PhaseRerun, Pyoemg

PyoEmgs

examples/biorbd/gait_reconstruction.py line 45 at r1 (raw file):

    for i_muscle in range(nb_muscles):
        fake_emg[i_muscle, :] = np.linspace(0.01, 1, nb_frames)
    pyoemg = Pyoemg(

PyoMuscles

examples/biorbd/gait_reconstruction.py line 46 at r1 (raw file):

        fake_emg[i_muscle, :] = np.linspace(0.01, 1, nb_frames)
    pyoemg = Pyoemg(
        data=fake_emg,

magnitude (?)

EveCharbie

Reviewable status: all files reviewed, 13 unresolved discussions (waiting on @Ipuch)

examples/biorbd/gait_reconstruction.py line 4 at r1 (raw file):